Research workbench
Crystal structure of lysyl-tRNA synthetase lysrs from burkholderia thailandensis bound to lysine
Analyse Crystal structure of lysyl-tRNA synthetase lysrs from burkholderia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EX5
- Type
- protein
- Length
- 972 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysine--tRNA ligase
- EC
- 6.1.1.6
- UniProt
- Q2SXD6
- Ligands
- LYS
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 486 | 38% helix, 27% strand | Q2SXD6 |
| B | Lysine--tRNA ligase (EC 6.1.1.6) | protein | 486 | 38% helix, 27% strand | Q2SXD6 |
Ligands and binding sites
- LYS · Lysine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.80 | 0.87 | 81 | empty |
| 2 | 689 | 0.75 | 0.81 | 64 | LYS |
| 3 | 668 | 0.75 | 0.81 | 60 | LYS |
| 4 | 161 | 0.60 | 0.83 | 24 | empty |
| 5 | 137 | 0.44 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 4584 Ų buried · 75 hydrogen bonds · protein-protein
Compared structures
- 4EX5 · Crystal structure of lysyl-tRNA synthetase LysRS from Burkholderia thailandensis bound to… · the same entry in another collection · chain B against B, TM-score 1.00
- Q2SXD6 · AlphaFold monomer V2.0 prediction for lysine--tRNA ligase (Q2SXD6) · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q2SXD6
- Elsewhere: RCSB PDB 4EX5 · PDBe 4EX5 · UniProt Q2SXD6
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